Thai jasmine rice, KDML 105, is known as the best quality rice. It is known not only for its aroma but also for its good cooking and eating qualities. Amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) are important traits determining rice quality. A population of recombinant inbred lines (RIL) derived from KDML105 × CT9993 cross was used to study the genetic control of AC, GC and GT traits. A total of 191 markers were used in the linkage map construction. The 1605.3 cM linkage map covering nearly the whole rice genome was used for QTL (define QTL) analysis. Four QTLs for AC were detected on chromosomes 3, 4, 6 and 7. These QTLs accounted for 80% of phenotypic variation explained (PVE) in AC. The presence of one major gene as well as several modifiers was responsible for the expression of the trait. Two QTLs on chromosome 6 and one on chromosome 7 were detected for GC, which accounts for 57% of PVE. A single gene of major effect along with modifier genes controls GC from this cross. The QTLs in the vicinity of waxy locus were major contributors in the expression of AC and GC. The finding that the position of QTLs for AC and GC were near each other may reflect tight linkage or pleiotropy. Three QTLs were detected, one on chromosome 2 and two on chromosome 6, which accounted for 67% of PVE in GT. Just like AC and GC, one major gene and modifier genes governed the variation in GT resulting from the KDML105 × CT9993 cross. Breeding for cooking and eating qualities will largely rely on the preferences of the end users.

Bph3, a major brown planthopper (BPH) resistance locus derived from the rice cultivar Rathu Heenati (RH), has been used as a stable donor of traits that improve highly susceptible aromatic rice varieties in Thailand. Map-based cloning was initiated using a set of isogenic lines (ILs) harboring the major Bph3 locus on chromosome 6. IL genomes were scanned with a 57 K Affymetrix Rice GeneChip to identify the gene responsible for Bph3. Single-feature polymorphism (SFP) mapping was used to localize 84 candidate genes. An expression analysis of 15 selected candidate genes in the aromatic rice cultivar KDML105 (KD) and the ILs under normal conditions revealed two differentially expressed sequences. Following hopper feeding, only one candidate gene, Os04g27430, was differentially expressed. Os04g27430 encodes a putative sesquiterpene synthase (STPS) gene that was induced by BPH feeding in ILs. An antixenosis test in three selected ILs revealed a major role for STPS in insect preference during the first 120 hours of the rice-insect interaction. Functional SNPs in exon 5 that resulted in the deletion of seven amino acids in the susceptible rice line were identified. Moreover, three additional SNPs associated with three transcription binding sites were also identified, which might explain the differential response of Os04g27430 during the anti-feeding test. Os04g27430 is the second known rice STPS induced by BPH. The gene may involve an antixenosis BPH resistance mechanism. The combination of the STPS and the Bph3 locus was more effective than Bph3 alone in the tested ILs.

Sweetness is an economically important eating quality trait for sweet-corn breeding. To investigate the genetic control of the sweetness trait, we conducted a genome-wide association study (GWAS) in an association panel consisting of 250 sweet corn and waxy corn inbred and recombinant inbred lines (RILs), together with the genotypes obtained from the high-density 600K maize genotyping single-nucleotide polymorphism (SNP) array. GWAS results identified 12 significantly associated SNPs on chromosomes 3, 4, 5, and 7. The most associated SNP, AX_91849634, was found on chromosome 3 with a highly significant p-value of ≤1.53 × 10⁻¹⁴. The candidate gene identified within the linkage disequilibrium (LD) of this marker was shrunken2 (Zm00001d044129; sh2), which encodes ADP-glucose pyrophosphorylase (AGPase), a 60 kDa subunit enzyme that affects starch metabolism in the maize endosperm. Several SNP markers specific to variants in sh2 were developed and validated. According to the validation in a set of 81 inbred, RIL, and popular corn varieties, marker Sh2_rs844805326, which was developed on the basis of the SNP at the position 154 of exon 1, was highly efficient in classifying sh2-based sweet corn from other types of corn. This functional marker is extremely useful for marker-assisted breeding in sh2-sweet corn improvement and marketable seed production.

Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to indica and japonica groups. The indica group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise F_ST showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding.